SensitivityPedons.knit

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## Sensitivity Analysis for Standard Profile Descriptions
 
 #### Implications for Soil Taxonomy, Interpretations, and Mapping
 
 
 
 #### FIELD NOTES WEBINAR - August 2021

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.right[.large[ 
 Andrew G. Brown 
 <a href="mailto:andrew.g.brown@usda.gov"><svg viewBox="0 0 576 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M160 448c-25.6 0-51.2-22.4-64-32-64-44.8-83.2-60.8-96-70.4V480c0 17.67 14.33 32 32 32h256c17.67 0 32-14.33 32-32V345.6c-12.8 9.6-32 25.6-96 70.4-12.8 9.6-38.4 32-64 32zm128-192H32c-17.67 0-32 14.33-32 32v16c25.6 19.2 22.4 19.2 115.2 86.4 9.6 6.4 28.8 25.6 44.8 25.6s35.2-19.2 44.8-22.4c92.8-67.2 89.6-67.2 115.2-86.4V288c0-17.67-14.33-32-32-32zm256-96H224c-17.67 0-32 14.33-32 32v32h96c33.21 0 60.59 25.42 63.71 57.82l.29-.22V416h192c17.67 0 32-14.33 32-32V192c0-17.67-14.33-32-32-32zm-32 128h-64v-64h64v64zm-352-96c0-35.29 28.71-64 64-64h224V32c0-17.67-14.33-32-32-32H96C78.33 0 64 14.33 64 32v192h96v-32z"></path></svg>&nbsp;andrew.g.brown@usda.gov</a>
 
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## Sensitivity and Uncertainty Analysis

**Sensitivity analysis**: Understand _sources_ of uncertainty

- Applying constraints to inform inferences about a system

**Uncertainty analysis**: Propagation and _quantification_ of uncertainty
 
 - "Overview of Soil Survey Database History with Uncertainty implications"
 - https://www.nrcs.usda.gov/Internet/FSE_DOCUMENTS/nrcs142p2_050742.pdf
 
 - NSSH 618.2.C Collecting, Testing, and Populating Soil Property Data
 - Original proposal to use percentiles for Range in Characteristics 
 https://github.com/ncss-tech/soil-range-in-characteristics

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## Soil Profile Geometry

- Soil descriptions as "emulators of natural variation"

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### Geometric Elements

- Location description / coordinates
- **Layer top and bottom depths**
- **Boundaries**
- Structure 
- Fragments / Artifacts
]

.pull-right[
![](data:image/png;base64,#img/ninigret.png)
_Source_: http://nesoil.com/ri/oldpedons/Ninigret_historic.pdf
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??? Soil descriptions as emulators of natural variation

Routine soil descriptions are aggregated to create soil survey products.

- In the past the individual points and source data were not considered the "product," yet there are increasing requests related to these data from soil survey users 
 
 - In update work, we are confronted with "changes" in soil properties due to level of detail in descriptions, new lab data, layers, taxonomic units and more.

- Are these "changes" meaningful in context of "similar soils"?
 - How can we systematically evaluate the similarity of soil concepts with different depth support?
 - How can we maximize value from historic data that may be cost-prohibitive to replicate?
 - How can we get more information from _new_ descriptions?
 
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## Discretization of the soil body

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![](data:image/png;base64,#img/minniecreek_pittape.jpg)

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![](data:image/png;base64,#img/minniecreek_golftees.jpg)

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## Discretization of the soil body
**Pedons** (source: FY2020 SQLite snapshots)
 - NASIS Pedon: 2,897,664 horizons in 573,919 NASIS pedons; ~5 layers each
 - KSSL/LDM: 410,011 horizons in 65,952 laboratory pedons; ~6.2 layers each
 
**Components** (source: Soil Data Access)
 - SSURGO: 3,474,612 horizons in 868,508 components; ~4 layers each
 - STATSGO: 333,388 horizons in 102,729 components; ~3.25 layers each
 
**GlobalSoilMap** 
 - 6 standard depth intervals: 
 0-5 cm, 5-15 cm, 15-30 cm, 30-60 cm, 60-100 cm and 100-200 cm
 - https://www.isric.org/sites/default/files/GlobalSoilMap_specifications_december_2015_2.pdf

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## Trends in "horizonation" schemes

![](data:image/png;base64,#img/complayer_by_year.png)

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## Horizon Boundaries

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#### Distinctness
![](data:image/png;base64,#img/boundary_distinctness.png)

#### Topography
![](data:image/png;base64,#img/boundary_topography.png)
]

.pull-right[
![](data:image/png;base64,#img/boundary_topography_drawing.png)
_Source_: [Field Book for Describing and Sampling Soils](https://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/research/guide/?cid=nrcs142p2_054184)
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## Soil Profile Sketches and Simulation with {aqp} R package

.left-column[
  [![](data:image/png;base64,#https://raw.githubusercontent.com/ncss-tech/aqp/master/misc/hexstickers/aqp_sticker_v2.png)](http://ncss-tech.github.io/aqp/)

[![](data:image/png;base64,#https://www.r-project.org/logo/Rlogo.png)](https://www.r-project.org/)
]

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The Algorithms for Quantitative Pedology (AQP) project is a suite of R packages for quantitative analysis of soil profile data. 
 - "aqp" package provides a vocabulary (functions and data structures)
 - "soilDB" package provides interfaces to databases and web services
 
AQP Website: http://ncss-tech.github.io/AQP/

aqp R package on GitHub: https://github.com/ncss-tech/aqp

SSSA 2020 Presentations: https://github.com/brownag/SSSA2020/
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## OSD Profile Sketches
.center[
Using representative depths as boundaries
<img src="data:image/png;base64,#SensitivityPedons_files/figure-html/unnamed-chunk-1-1.png" width="504" />
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## OSD Profile Sketches + distinctness
.center[
Using `aqp::hzDistinctnessCodeOffset()`
<img src="data:image/png;base64,#SensitivityPedons_files/figure-html/unnamed-chunk-2-1.png" width="504" />
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## Generalization of Horizons

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Using regular expressions to group similar horizons with `aqp::generalize.hz()`
<img src="data:image/png;base64,#SensitivityPedons_files/figure-html/unnamed-chunk-3-1.png" width="504" />
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## Horizon Boundary Sketches

_Source_: https://ncss-tech.github.io/AQP/aqp/hz-boundaries.html
![](data:image/png;base64,#img/boundary_types.png)

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## Perturbation-based Methods

.pull-left[
 - [`aqp::perturb()`](http://ncss-tech.github.io/aqp/docs/reference/perturb.html) "Perturbs" the _boundary thickness between horizons_ or the _thickness of horizons_ using a standard deviation specified as a horizon-level attribute. 
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By the empirical rule:
 - 68% of the boundary/horizon thicknesses within 1 standard deviation of source
 - 95% within 2 standard deviations
 - 99.7% within 3 standard deviations
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Distributional assumption applies only to the _geometry_. Not horizon or aggregate "site level" properties.

- Documentation: http://ncss-tech.github.io/aqp/docs/reference/perturb.html
 
 - Demo: https://ncss-tech.github.io/AQP/aqp/perturb.html
 
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## Thickness of Generalized Horizons
n=1000 realizations for each of 4 profiles ("Minniecreek" full pedons in CA649)
![](data:image/png;base64,#img/thickness_genhz.png)

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## Organic Carbon Stocks
n=10,000 aggregate carbon stocks; constant 2.5cm standard deviation  
![](data:image/png;base64,#img/carbon_stocks_lab.png)

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## Organic Carbon Stocks

n=10,000 aggregate carbon stocks using field horizon boundary distinctness
![](data:image/png;base64,#img/carbon_stocks_lab_distinctness.png)

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## "Problems"

### "Narrow" or disturbed observation methods (probe, bucket auger)

### Irregular and Broken Topography

### Total Soil Depth

### Integrating results from multiple pedons -> component and series decisions

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## Thank you!

Feel free to contact me with comments/questions/criticism.

We also welcome you to take part in discussions related to {aqp} algorithms and {soilDB} data access methods on the GitHub issues pages:

- https://github.com/ncss-tech/aqp/issues
 
 - https://github.com/ncss-tech/soilDB/issues

_USDA is an equal opportunity provider, employer, and lender._

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 ![](data:image/png;base64,#https://github.com/brownag.png)
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.right-column[
  #### Andrew G. Brown

<a href="mailto:andrew.g.brown@usda.gov"><svg viewBox="0 0 576 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M160 448c-25.6 0-51.2-22.4-64-32-64-44.8-83.2-60.8-96-70.4V480c0 17.67 14.33 32 32 32h256c17.67 0 32-14.33 32-32V345.6c-12.8 9.6-32 25.6-96 70.4-12.8 9.6-38.4 32-64 32zm128-192H32c-17.67 0-32 14.33-32 32v16c25.6 19.2 22.4 19.2 115.2 86.4 9.6 6.4 28.8 25.6 44.8 25.6s35.2-19.2 44.8-22.4c92.8-67.2 89.6-67.2 115.2-86.4V288c0-17.67-14.33-32-32-32zm256-96H224c-17.67 0-32 14.33-32 32v32h96c33.21 0 60.59 25.42 63.71 57.82l.29-.22V416h192c17.67 0 32-14.33 32-32V192c0-17.67-14.33-32-32-32zm-32 128h-64v-64h64v64zm-352-96c0-35.29 28.71-64 64-64h224V32c0-17.67-14.33-32-32-32H96C78.33 0 64 14.33 64 32v192h96v-32z"></path></svg>&nbsp;andrew.g.brown@usda.gov</a> 
<a href="http://github.com/brownag"><svg viewBox="0 0 496 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"></path></svg>&nbsp;brownag</a>

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